Locus 3445

Sequence ID 3R_DroMel_CAF1
Location 9,335,043 – 9,335,184
Length 141
Max. P 0.869873
window5530 window5531

overview

Window 0

Location 9,335,043 – 9,335,145
Length 102
Sequences 6
Columns 107
Reading direction forward
Mean pairwise identity 77.43
Mean single sequence MFE -24.50
Consensus MFE -10.92
Energy contribution -11.42
Covariance contribution 0.50
Combinations/Pair 1.00
Mean z-score -2.06
Structure conservation index 0.45
SVM decision value 0.07
SVM RNA-class probability 0.566549
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 9335043 102 + 27905053
AUCAGAGUAGUUUAGUGUGUUACUUUGUUGGUCACCGGCAAACUUUCUCGGCCAGCAG-UUACAUGGGCUUCAAACCUAUGUACAAACUUAUA----UAUAUACACC
..............((((((....(((((((((................)))))))))-.((((((((.......))))))))..........----...)))))). ( -23.59)
>DroPse_CAF1 103824 84 + 1
AUCAGAGUAGUUUCGUGUGUUACUUUGUUGGUCGGUGGCAAACUUUGUCGGCCAUCUGUAUAUAUU-------UAUGUA------------CA----UAUAUACAAC
..((((((((.........)))))))).(((((((..(......)..)))))))..(((((((((.-------......------------.)----)))))))).. ( -22.20)
>DroSec_CAF1 107341 91 + 1
AUCAGAGUAGUUUAGUGUGUUACUUUGUUGGUCGCUGGCAAACUUUCUCGGCCAGCAG-AU-------CUCCCAACCUAUGUACA----UGCA----UAUAUACACC
......(((.....((((((.((...(((((((((((((...........)))))).)-).-------...)))))....)))))----))).----....)))... ( -23.40)
>DroSim_CAF1 116615 98 + 1
AUCAGAGUAGUUUAGUGUGUUACUUUGUUGGUCGCUGGCAAACUUUCUCGGCCAGCAG-AUACAUGGGCUCCCAACCUAUGUACA----UACA----UAUAUACACC
......(((.....(((((....(((((((((((..((....))....))))))))))-)((((((((.......))))))))))----))).----....)))... ( -28.80)
>DroEre_CAF1 107252 102 + 1
AUCAGAGUAGUUUAGUGUGUUACUUUGUUGGUCGCCUGCAAACUUUCUCGGCCAGCAG-AUACAUGGGCUCACAACCUAUGUACA----UACAUACUCGUAUAUACC
....(((((.....(((((....(((((((((((..............))))))))))-)((((((((.......))))))))))----))).)))))......... ( -30.84)
>DroYak_CAF1 107527 83 + 1
AUCAGAGUAGUUUAGUGUGUUACUUUGUUGGUCGCCGGCAAACUUUCUCGGCCCGCAU-AUAUAU---------------GUAUA----AAUA----UGUAUAUACC
..((((((((.........))))))))..(((.((.(((...........))).))((-((((((---------------((...----.)))----)))))))))) ( -18.20)
>consensus
AUCAGAGUAGUUUAGUGUGUUACUUUGUUGGUCGCCGGCAAACUUUCUCGGCCAGCAG_AUACAUG__CUCCCAACCUAUGUACA____UACA____UAUAUACACC
...(((((((.........)))))))((((((((..............))))))))................................................... (-10.92 = -11.42 +   0.50)

alignment

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secondary structure

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dotplot

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Window 1

Location 9,335,083 – 9,335,184
Length 101
Sequences 5
Columns 105
Reading direction forward
Mean pairwise identity 80.78
Mean single sequence MFE -24.27
Consensus MFE -12.53
Energy contribution -15.00
Covariance contribution 2.47
Combinations/Pair 1.10
Mean z-score -2.38
Structure conservation index 0.52
SVM decision value 0.87
SVM RNA-class probability 0.869873
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 9335083 101 + 27905053
AACUUUCUCGGCCAGCAGUUACAUGGGCUUCAAACCUAUGUACAAACUUAUA----UAUAUACACCAGCCCGUAUAUACAGCCUUGGGUAGUUUGUGUGCCAUAU
.........(((((.....((((((((.......))))))))((((((....----(((((((........)))))))..(((...))))))))))).))).... ( -24.30)
>DroSec_CAF1 107381 90 + 1
AACUUUCUCGGCCAGCAGAU-------CUCCCAACCUAUGUACA----UGCA----UAUAUACACCAGCCCGUAUAUACAGCCUUGGGUAGUUUGUGUGCCAUAU
.........(((..((((((-------..(((((....((((.(----(((.----...............)))).))))...)))))..))))))..))).... ( -23.49)
>DroSim_CAF1 116655 97 + 1
AACUUUCUCGGCCAGCAGAUACAUGGGCUCCCAACCUAUGUACA----UACA----UAUAUACACCGGCCCGUAUAUACAGCCUUGGGUAGUUUGUGUGCCAUAU
.........(((........((((..((((((((..(((((...----.)))----))........(((..((....)).)))))))).)))..))))))).... ( -24.50)
>DroEre_CAF1 107292 101 + 1
AACUUUCUCGGCCAGCAGAUACAUGGGCUCACAACCUAUGUACA----UACAUACUCGUAUAUACCAGCCUGUAUAUACAGCCUUGUGUAGUUUGUGCGCCAUAU
.........(((..(((((((((((((((.......(((((...----.)))))...((((((((......)))))))))))).))))).))))))..))).... ( -29.00)
>DroYak_CAF1 107567 82 + 1
AACUUUCUCGGCCCGCAUAUAUAU---------------GUAUA----AAUA----UGUAUAUACCAGCCCUUAUAUACAGCCUUGGGUAGUUUGUGUGCCAUAU
.........(((.(((((((((((---------------((...----.)))----)))))))....((((..............)))).....))).))).... ( -20.04)
>consensus
AACUUUCUCGGCCAGCAGAUACAUGGGCUCCCAACCUAUGUACA____UACA____UAUAUACACCAGCCCGUAUAUACAGCCUUGGGUAGUUUGUGUGCCAUAU
.........(((..(((((((((((((.......)))))))..........................(((((............))))).))))))..))).... (-12.53 = -15.00 +   2.47)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:01:13 2006